PLUMED-NEST

Project ID: plumID:21.047
Source: Aluminum/950K-MetaD/plumed.dat
Originally used with PLUMED version: 2.8
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

RESTARTActivate restart. More details

The RESTART action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../../PairEntropy.cpp

PAIRENTROPYCalculate the KL Entropy from the radial distribution function More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=s2The PAIRENTROPY action with label s2 calculates the following quantities:
 Quantity   
 Type   
 Description  
s2
scalar
the value calculated by this action
 ATOMSthe atoms that are being used to calculate the RDF=1-256
 MAXRthe maximum distance to use for the rdf=0.7
 SIGMA an alternative method for specifying the bandwidth instead of using the BANDWIDTH keyword=0.0125
... PAIRENTROPY

ENERGYCalculate the total potential energy of the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy

VOLUMECalculate the volume the simulation box. More details LABELa label for the action so that its output can be referenced in the input to other actions=volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box

COMBINECalculate a polynomial combination of a set of other variables. More details ...
 ARGthe values input to this function=ene,vol
 POWERS the powers to which you are raising each of the arguments in your function=1,1
 COEFFICIENTS the coefficients of the arguments in your function=1.,0.060221409
 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
 LABELa label for the action so that its output can be referenced in the input to other actions=enthalpyThe COMBINE action with label enthalpy calculates the following quantities:
 Quantity   
 Type   
 Description  
enthalpy
scalar
a linear compbination
... COMBINE

COMBINECalculate a polynomial combination of a set of other variables. More details ...
 ARGthe values input to this function=enthalpy
 POWERS the powers to which you are raising each of the arguments in your function=1
 COEFFICIENTS the coefficients of the arguments in your function=0.00390625
 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
 LABELa label for the action so that its output can be referenced in the input to other actions=enthalpyPerAtomThe COMBINE action with label enthalpyPerAtom calculates the following quantities:
 Quantity   
 Type   
 Description  
enthalpyPerAtom
scalar
a linear compbination
... COMBINE

METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
 ARGthe labels of the scalars on which the bias will act=enthalpyPerAtom,s2
 SIGMAthe widths of the Gaussian hills=0.3,0.1
 HEIGHTthe heights of the Gaussian hills=7.5
 BIASFACTORuse well tempered metadynamics and use this bias factor=30
 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=950.0
 PACEthe frequency for hill addition=500
 GRID_MINthe lower bounds for the grid=-325,-12
 GRID_MAXthe upper bounds for the grid=-285,-1
 GRID_BINthe number of bins for the grid=500,500
 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
 LABELa label for the action so that its output can be referenced in the input to other actions=metad
 ARGthe labels of the scalars on which the bias will act=enthalpyPerAtom,s2
 SIGMAthe widths of the Gaussian hills=0.3,0.1
 HEIGHTthe heights of the Gaussian hills=7.5
 BIASFACTORuse well tempered metadynamics and use this bias factor=30
 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=950.0
 PACEthe frequency for hill addition=500
 GRID_MINthe lower bounds for the grid=-325,-12
 GRID_MAXthe upper bounds for the grid=-285,-1
 GRID_BINthe number of bins for the grid=500,500
 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 FILE a file in which the list of added hills is stored=HILLS
... METAD

PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR